TTLL9

tubulin tyrosine ligase like 9, the group of Tubulin tyrosine ligase family

Basic information

Region (hg38): 20:31870634-31945000

Previous symbols: [ "C20orf125" ]

Links

ENSG00000131044 ∙ NCBI:164395 ∙ OMIM:619838 ∙ HGNC:16118 ∙ Uniprot:Q3SXZ7 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• male infertility with azoospermia or oligozoospermia due to single gene mutation (Moderate), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TTLL9 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TTLL9 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			22			22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	23	0	0

Variants in TTLL9

This is a list of pathogenic ClinVar variants found in the TTLL9 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
20-31887215-A-T		not specified	Uncertain significance (May 18, 2023)
20-31898525-G-A		not specified	Uncertain significance (Jun 29, 2022)
20-31908608-T-G		not specified	Uncertain significance (Jan 16, 2024)
20-31908650-A-G		not specified	Uncertain significance (May 31, 2023)
20-31908656-A-G		not specified	Uncertain significance (Jul 19, 2023)
20-31908673-C-T		not specified	Uncertain significance (Nov 12, 2021)
20-31908689-G-T		not specified	Uncertain significance (Apr 18, 2023)
20-31909744-G-A		not specified	Uncertain significance (Sep 16, 2021)
20-31909779-C-T		not specified	Uncertain significance (Apr 27, 2023)
20-31909789-T-G		not specified	Uncertain significance (Oct 05, 2023)
20-31909860-G-A		not specified	Uncertain significance (May 09, 2023)
20-31919868-C-A		not specified	Uncertain significance (Jan 11, 2023)
20-31919879-G-A		not specified	Uncertain significance (Sep 20, 2023)
20-31919891-T-C		not specified	Uncertain significance (Nov 08, 2022)
20-31919907-T-C		not specified	Uncertain significance (Sep 01, 2021)
20-31922980-C-A		not specified	Uncertain significance (Apr 22, 2022)
20-31922981-G-A		not specified	Uncertain significance (Nov 22, 2021)
20-31923047-A-T		not specified	Uncertain significance (Feb 27, 2024)
20-31925012-G-A		not specified	Uncertain significance (Mar 20, 2024)
20-31925046-G-A		not specified	Uncertain significance (May 13, 2024)
20-31937396-G-A		not specified	Likely benign (May 10, 2024)
20-31937400-C-A		not specified	Uncertain significance (Jun 14, 2023)
20-31937447-A-T		not specified	Uncertain significance (Jun 10, 2024)
20-31937481-A-G		not specified	Uncertain significance (Aug 26, 2022)
20-31937482-C-A		not specified	Uncertain significance (Aug 10, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TTLL9	protein_coding	protein_coding	ENST00000375938	14	74260

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.20e-18	0.00907	124656	0	155	124811	0.000621

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.436	250	270	0.925	0.0000166	2905
Missense in Polyphen		88	101.8	0.86444		1072
Synonymous	1.21	85	100	0.846	0.00000617	789
Loss of Function	0.318	28	29.9	0.937	0.00000153	326

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00165	0.00158
Ashkenazi Jewish	0.0000993	0.0000993
East Asian	0.000613	0.000612
Finnish	0.0000464	0.0000464
European (Non-Finnish)	0.000604	0.000600
Middle Eastern	0.000613	0.000612
South Asian	0.000590	0.000588
Other	0.00165	0.00165

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probable tubulin polyglutamylase that forms polyglutamate side chains on tubulin. Probably acts when complexed with other proteins (By similarity). {ECO:0000250}.
• Pathway: Post-translational protein modification;Metabolism of proteins;Carboxyterminal post-translational modifications of tubulin (Consensus)

Recessive Scores

• pRec: 0.113

Intolerance Scores

• loftool: 0.820
• rvis_EVS: 0.42
• rvis_percentile_EVS: 77.23

Haploinsufficiency Scores

• pHI: 0.236
• hipred: N
• hipred_score: 0.325
• ghis: 0.542

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.206

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Ttll9

Gene ontology

• Biological process: cellular protein modification process
• Cellular component: cytoplasm;microtubule;cilium
• Molecular function: ATP binding;ligase activity